lazear
QC metrics
Dear Sage Developers, We are currently looking into the possibility of integrating SAGE into our QC procedure.
What we currently do is using HEK runs (DIA) which we run through DIA-NN automatically. DIA-NN has a nice little overview of most relevant metrics in a stats.tsv file.
If you are not familiar: It is a very short tsv output that lists the analyzed raw file, number of IDs (precs, prots), MS1 /MS2 signal aggregation, FWHM of peaks, mass accuracy and some other stuff.
We have extended this to also catch IM shifts in timsTOF data.
However, we now need to extend this pipeline to also be able to analyse DDA data.
Is it somehow possible to extract these info or some of them from SAGE? I can currently not find it in the outputs, also when I specify LFQ.... What would be especially helpful is chromatographic peak width, eg as FWHM readout.
SAGE would be an extremely cool option to do comprehensive QCs, as it is so light weight and fast.
Any input would be welcome!
Best, K
Hi Klemens,
I like the idea! This might be a good feature for a new contributor to work on too - let me see if I can find someone, otherwise I will try and tackle it.
Hi,
Just wanted to add to this, I was also thinking it would be nice to have an html report file of some QC plots. I just recently wrote a simple html report builder redeem-classifiers/src/report/report.rs as part of a rust library that I wrote for implementing/loading deep learning models and semi-supervised classifier PSM scoring models.
I have this currently integrated in Bruker's private internal Sage repo (still testing some integration with the deep learning stuff), but I could separate out the report generation and make a PR to the public repo if that is of interest?
I currently just generate a few interactive plots for QC of the PSM scoring. I did add a downloadable table to the results overview section. I could add a few more metrics, just would need to know what other metrics you would like.
Best,
Justin
